Approximate Chemical Modeling Methods--Chemistry 7711/8711
Instructor: Dr. Abby Parrill
General Course Information
- Syllabus
- Semester Calendar
- Second Peer Review Form (Research Update)
- Conformational distribution sample spreadsheet
- Coupling constants from torsion angles sample spreadsheet
Class Notes 2004
- Topic 1: Introduction, Visualization and Public Structure Databases (Handout)
- Topic 2: Molecular Mechanics (Handout)
- Topic 3: Geometry Optimization (Handout, updated 9/10/04)
- Topic 4: Conformational Searching (Handout, updated 9/10/04)
- Topic 5: Coarse-Grained Modeling (Handout, updated 10/20/04)
- Topic 6: Energetics (Handout, updated 9/21/04)
- Topic 7: Guiding Conformational Searches with Experimental Information (Handout, updated 9/21/04)
- Topic 8: Molecular Dynamics (Handout, updated 9/28/04)
- Topic 9: Solvation (Handout, updated 9/30/04)
- Topic 10: Protein Modeling (Handout, updated 10/18/04)
- Topic 11: QSAR (Handout, updated 10/18/04)
- Topic 12: Docking (Handout, updated 10/20/04)
- Topic 13: De novo design (Handout, updated 10/26/04)
- Topic 14: Transition State Modeling (Handout)
- Topic 15: Modeling Lipids and DNA (Handout)
- Topic 16: Combined Methods - QM/MM
- Topic 17: Clustering and Combinatorial Chemistry (Handout, updated 11/29/2004)
- Topic 18: Forcefield Parameterization (Handout, updated 11/29/2004)
- Topic 19: Modeling Organometallic Systems in the MM Formalism (Handout, updated 11/29/2004)
- Topic 20: Artificial Intelligence in Chemistry (Handout, updated 11/29/2004)
- Topic 21: Introduction to Unix (Handout, updated 11/29/2004)
Helpful Web Resources
- The Protein Databank
- GeneBank
- Cambridge Crystallographic Data Centre
- Reciprocal.net - a distributed crystallography network for researchers, students and the general public